Proteomics of protein trafficking by in vivo tissue-specific labeling

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Acknowledgement

I.A.D. acknowledges generous financial support from NSERC PGS-M and PGS-D, Brigham and Women’s Hospital Osher Pre-doctoral fellowship, and Harvard Medical School (HMS) Department of Cell Biology Innovative Grant Program (IGP). We thank Aldina Mesic and the Microscopy Resources on the North Quad (MicRoN) core at HMS for excellent technical assistance. We thank the Janelia Gene Targeting and Transgenics Facility (Director: Caiying Guo) for the mESC generation. We thank Seung Kim, Andreas Brech, Akhila Rajan, TRiP at HMS, VDRC, Bloomington Drosophila Resource Center, and Developmental Studies Hybridoma Bank for stocks and antibodies. N.P. is an investigator of the Howard Hughes Medical Institute (HHMI). We acknowledge the National Institutes of Health (NIH) grants 5P01CA120964 (J.M.A.) and 5P30CA006516 (J.M.A.). This work was supported by an HCIA grant from HHMI, NIGMS P41 GM132087 to N.P., and the NIH Transformative R01 grant 5R01DK121409 to A.P.M., A.Y.T., S.A.C., and N.P.

Funding

We acknowledge the National Institutes of Health (NIH) grants 5P01CA120964 (J.M.A.) and 5P30CA006516 (J.M.A.). This work was supported by an HCIA grant from HHMI, NIGMS P41 GM132087 to N.P., and the NIH Transformative R01 grant 5R01DK121409 to A.P.M., A.Y.T., S.A.C., and N.P.

Contributions

I.A.D. conceived the initial Drosophila method and study, and I.A.D., A.P.M., and N.P. conceived the extension of the approach to mammals. I.A.D., A.S.M., A.P.M., and N.P. designed and supervised experiments. I.A.D., D.W., A.S.M., R.Y., J.A.M., J.G., N.D.U., L.M., D.K.C., D.R., T.S., R.Z., A.T., and J.M.A. performed experiments. I.A.D., D.W., A.S.M., R.Y., J.M., Y.H., N.D.U., L.M., D.K.C., T.S., J.M.A., S.A.C., A.P.M., and N.P. analyzed data. T.B. and A.Y.T. generated BirA*G3, and J.A.B. cloned it into Drosophila. I.A.D, A.S.M., and N.P. wrote the manuscript with input from all authors.

Data Availability

The original mass spectra for all experiments, and the protein sequence databases used for searches have been deposited in the public proteomics repository MassIVE (https://massive.ucsd.edu) and are accessible at https://doi.org/10.25345/C5NB8W with the accession number MSV000086664 (mouse and fly BirA* data sets), and at https://doi.org/10.25345/C5XN4Z with the accession number MSV000086291 (fly hemolymph data sets). The following publicly available data sets/databases were used: UniProt database (https://www.uniprot.org/; Drosophila (DROME; https://www.uniprot.org/proteomes/UP000000803), mouse (https://www.uniprot.org/proteomes/UP000000589), and human (https://www.uniprot.org/proteomes/UP000005640)), DIOPT (https://www.flyrnai.org/cgi-bin/DRSC_orthologs.pl), GLAD (https://www.flyrnai.org/tools/glad/web/), Signaling Receptome (http://www.receptome.org/), human plasma proteome data sets (http://www.peptideatlas.org/repository/repository_public_Hs_Plasma2.php (PeptideAtlas) and Supplementary Table 1 in ref. ⁶¹), SignalP database (http://www.cbs.dtu.dk/services/SignalP/ and http://www.cbs.dtu.dk/services/SignalP-4.1/), Drosophila mitochondrial proteome (Supplementary Data 1 in ref. ⁵²), TMHMM (http://www.cbs.dtu.dk/services/TMHMM/), SecretomeP (http://www.cbs.dtu.dk/services/SecretomeP/), FlyAtlas microarray (http://flyatlas.org/atlas.cgi), Drosophila RNAseq (http://www.modencode.org/celniker/), PAXdb (https://pax-db.org/), NCBI Gene (https://www.ncbi.nlm.nih.gov/gene/), FlyBase (https://flybase.org/), mammalian adipocyte secretomes (Tables S1–S5 in ref. ⁷, Supplementary Data Table C in ref. ⁷⁰, Supplementary Data Table in ref. ⁷¹, Supplementary Table S1 in ref. ⁷², Supplementary Table—Secretome in ref. ⁷³, Supplementary Table S1 in ref. ⁷⁴, Data File S1 in ref. ⁷⁵, Table 2 and Supplementary Table 1 in ref. ⁷⁷, Supplementary Table 2A in ref. ⁷⁸), mammalian myocyte secretomes (Table 1 in ref. ⁷⁹, Supplementary Table S1 in ref. ⁸⁰, Supplementary Table 1 in ref. ⁸¹, Supplementary Table 1 in ref. ⁸², Table 2 in ref. ⁸³, Supplementary Table S1 in ref. ⁸⁴, Table S5 in ref. ⁸⁵, Supplementary Table S1 in ref. ⁸⁶). The main text and supplementary information shows all of the data collected as part of this work. The corresponding authors will provide original data on reasonable request. Source data are provided with this paper.

Supplemental Material